Package pal.eval

Class ChiSquareValue

  • All Implemented Interfaces:
    MultivariateFunction
    public class ChiSquareValue
extends java.lang.Object
implements MultivariateFunction
    computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix
    Version:
    $Id: ChiSquareValue.java,v 1.14 2002/12/05 04:27:28 matt Exp $
    Author:
    Korbinian Strimmer

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double compute()
      compute (weighted) least-square value for current tree (fixed branch lengths) return chi-square value
      double evaluate​(double[] params)
      compute (weighted) least-squares value
      double getLowerBound​(int n)
      get lower bound of argument n
      int getNumArguments()
      get number of parameters in tree
      OrthogonalHints getOrthogonalHints()  
      Tree getTree()
      Returns the (parameterized) tree of this likelihood value.
      double getUpperBound​(int n)
      get upper bound of argument n
      double optimiseParameters()
      optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
      double optimiseParameters​(MultivariateMinimum mm)
      optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
      void setTree​(Tree t)
      define (parameterized) tree

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • ChiSquareValue

        public ChiSquareValue​(DistanceMatrix m,
                      boolean w)
        initialization
        Parameters:
        m - distance matrix
        w - determines whether weighted or unweighted chi-squares are computed

    • Method Detail

      • setTree

        public void setTree​(Tree t)
        define (parameterized) tree
        Parameters:
        t - tree

      • getTree

        public Tree getTree()
        Returns the (parameterized) tree of this likelihood value.

      • compute

        public double compute()
        compute (weighted) least-square value for current tree (fixed branch lengths) return chi-square value

      • optimiseParameters

        public double optimiseParameters()
        optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
        Returns:
        minimimum chi-square value

      • optimiseParameters

        public double optimiseParameters​(MultivariateMinimum mm)
        optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
        Parameters:
        mm - optimiser for ParameterizedTree
        Returns:
        minimum chi-square value

      • evaluate

        public double evaluate​(double[] params)
        compute (weighted) least-squares value
        Specified by:
        evaluate in interface MultivariateFunction
        Parameters:
        params - parameters (branch lengths) of the tree
        Returns:
        function value

      • getNumArguments

        public int getNumArguments()
        get number of parameters in tree
        Specified by:
        getNumArguments in interface MultivariateFunction
        Returns:
        number of parameters